NCBO VIRTUAL APPLIANCE v2.0 FAQ

This FAQ now covers the NCBO Virtual Appliance v2.0. The FAQ for v1.0 is available in the archive

Ontology Management

How do I add or change categories or groups?

There is currently no UI administrator interface (though this will likely be added in future versions). Categories and groups can be added using a console after logging into the Appliance as the root user.

How can I migrate ontologies from BioPortal or previous NCBO Virtual Appliance versions into a new Appliance?

Programmatic migrations are currently unsupported. Ontologies can be manually downloaded and added using the Web UI.

Ontology Parsing

When are new ontologies parsed?

The ncbo_cron project uses a scheduler to run a process that collects new ontology submissions and parses them, adds them to the search index, calculates metrics, and processes them for use with the annotator. You can also parse ontologies manually.

How do I manually parse an ontology?

To manually parse an ontology, you will need to interact with the code using the console:

How do I know if an ontology has parsed?

The BioPortal Web UI will cache information about ontologies for 60 seconds. After parsing is complete, just refresh the ontology summary page to see the status for the most recent submission listed under the "Submissions" table.

In addition, you can look at the REST service directly, which will always give you the most updated information. To do this, visit the following URL:

How can I use the Appliance on Amazon EC2?

The NCBO Virtual Appliance can be deployed in Amazon EC2. The AMI is available in US West (Northern California) region, has the id ami-f7e8c7b2 and is built on the EBS-backed 64-bit Amazon Linux AMI 2013.03

Installation Instructions

Click on Launch Instances which will bring up Launch Instance Wizard with multiple tabs.

1. Choose AMI:

Select Community AMIs and search of “NCBO Appliance” and choose the latest version

2. Choose Instance Type Tab

Instance Type = General Purpose m1.xlarge (or any other type with at least 4 vCPUs and ~8 GB of RAM)

3. Configure Instance Tab

Availability Zone = No preference

Termination Protection = Prevention against accidental termination

Shutdown Behavior = Stop

5. Instance Tags:

Name = Name this instance something meaningful

6. Configure Security Group

Choose (you may need to create one first) a Security Group that has ports 22, 80, and 8082 open. It is recommended that you only allow the networks you need. We accept no responsibility/liability for machines getting compromised.

Click "Launch"
You will have to create or choose an existing Key Pairs or Create a Key Pair.

Click on Instances (left hand side of the screen):

Once the instance State has changed from Pending to Running and Status Checks is “2/2 checks passed”, login to the instance via the public hostname provided.

Now you can SSH into the machine using your key-pair and ec2-user as the user name:

ssh -i yourkey_pair ec2-user@{amazon public domain name}

The domain name can be retrieved by clicking on the instance and looking at the details that appear at the bottom of the screen. It should look similar to this but with a different set of numbers in the subdomain: ec2-10-0-0-1.us-west-1.compute.amazonaws.com